[gmx-users] grompp problem

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 15 13:41:28 CET 2007

> Hi all,
> To work with PTR in gromacs I added the residue information in
> ffG53a6.rtp, added the unknown atom names () to  ffG53a6.atp and
> added the residue name to aminoacids.dat.
> this allowed me to make the topology file  using pdb2gmx, create the
> box and fill it with water.  Now I want to perform the energy
> minimisation by first doing grompp.

Good problem description, but what was your command line, the location of
these files you edited and the value of GMXRC? I'm surmising that gromacs
isn't finding the .atp you changed.


>  Then
> I get an error
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> Cleaning up temporary file grompp8BMpzT
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toputil.c, line: 61
> Fatal error:
> Atomtype 'CB' not found!
> -------------------------------------------------------
> Yet I added the atom CB to the ffG53a6.atp file ... so what can be
> the problem here?
> Tom
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